Generation of induced pluripotent stem cells (iPSCs) holds great promise to regenerative medicine. However, before this technology can be applied for clinical purpose, the issues of iPSC efficiency and safety need to be addressed. In this study, we have compared a simple TAT- and 11 arginine (R)-protein transduction domain (PTD) for somatic cell reprogramming and explored the optimal conditions for the PTD to transduce reprogramming factors (RFs). We show that all recombinant TAT- and 11R-fused RFs are transcriptionally active as they activate their corresponding reporter genes in reporter assays. The TAT-RFs are in general transcriptionally more active than the corresponding 11R-RFs, but less active than the corresponding retroviral transduced RFs. Furthermore, each of TAT-RFs can substitute for their corresponding retrovirus in reprogramming. Finally, using five TAT-RFs together with an HDAC inhibitor, we can generate iPSC-like colonies from human fibroblast cells with high efficiency approximately 2 weeks after the first protein transduction. These colonies exhibit unique features of pluripotent stem cells including the morphology and the expression of pluripotency-associated markers. This characterization of recombinant RFs in reprogramming should facilitate the generation of clinically useful and genetic material-free human iPSCs.